Project Members:
Prof. Dr. Verena Keitel
verena.keitel@med.uni-duesseldorf.de
Universitätsklinikum Düsseldorf
Dr. Maria Reich
maria.reich@uni-duesseldorf.de
Universitätsklinikum Düsseldorf
Prof. Dr. Mathias Heikenwälder
m.heikenwaelder@dkfz-heidelberg.de
DKFZ Heidelberg
QBiC contacts:
Dr. Gisela Gabernet
Bioinformatics project manager
gisela.gabernet@qbic.uni-tuebingen.de
The pathway analysis results are stored here, and explained in this section.
The plot below summarizes the pathways that were found significantly enriched in DE genes for each contrast (padj value < 0.05). Only contrasts for which an enriched pathway was found are shown. Both KEGG pathways and REACTOME (REAC) pathways were considered.
Hover over the dots to reveal the pathway names.
Table summarizing all the enriched pathways. The results can also be inspected on the browser query under this link: https://biit.cs.ut.ee/gplink/l/VMSJLd0yTj. This table can be also found under pathway_analysis.
| Contrast | Pathway name | Pathway code | DE genes in pathway (N) | Total genes in pathway (N) | Fraction of DE genes in pathway | Padj value (pathway enrichment) | DE genes names |
|---|---|---|---|---|---|---|---|
| DE_genes_Cholangiocytes_KO_vs_WT | Complement and coagulation cascades | KEGG:04610 | 15 | 91 | 0.165 | 1e-07 | C3,Serpina1b,Serpina1a,Serpina1d,Serpind1,Serpina1c,Cfb,Cpb2,F2,Vtn,Kng2,C4bp,Fgg,Cfi,Fga |
| DE_genes_Cholangiocytes_KO_vs_WT | Steroid biosynthesis | KEGG:00100 | 7 | 20 | 0.35 | 1.29e-05 | Sqle,Cyp51,Fdft1,Msmo1,Nsdhl,Dhcr7,Sc5d |
| DE_genes_Cholangiocytes_KO_vs_WT | Terpenoid backbone biosynthesis | KEGG:00900 | 6 | 23 | 0.261 | 0.000731 | Hmgcr,Fdps,Idi1,Hmgcs1,Mvd,Pmvk |
| DE_genes_Cholangiocytes_KO_vs_WT | Cell adhesion molecules | KEGG:04514 | 13 | 162 | 0.0802 | 0.00541 | Cldn10,Cldn8,H2-T23,H2-Q6,H2-D1,H2-Q7,H2-K1,Cldn2,Cdh2,Vcam1,Itgav,Icam1,Cldn4 |
| DE_genes_Cholangiocytes_KO_vs_WT | Human T-cell leukemia virus 1 infection | KEGG:05166 | 15 | 236 | 0.0636 | 0.0209 | Fdps,H2-T23,H2-Q6,H2-D1,H2-Q7,H2-K1,Ccnd2,Creb3l3,Zfp36,Tgfb2,Ran,Tspo,Trp53,Nfkbia,Icam1 |
| DE_genes_Cholangiocytes_KO_vs_WT | Kaposi sarcoma-associated herpesvirus infection | KEGG:05167 | 14 | 217 | 0.0645 | 0.029 | C3,H2-T23,H2-Q6,Ubc,H2-D1,Vegfa,H2-Q7,H2-K1,Stat1,Zfp36,Trp53,Ifngr1,Nfkbia,Icam1 |
| DE_genes_Cholangiocytes_KO_vs_WT | AGE-RAGE signaling pathway in diabetic complications | KEGG:04933 | 9 | 99 | 0.0909 | 0.03 | Vegfa,Ccl2,Stat1,Vcam1,Tgfb2,Fn1,Agt,Icam1,Col4a1 |
| DE_genes_Cholangiocytes_KO_vs_WT | Proteasome | KEGG:03050 | 6 | 47 | 0.128 | 0.05 | Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Cholangiocytes_KO_vs_WT | Cholesterol biosynthesis | REAC:R-MMU-191273 | 12 | 25 | 0.48 | 6.84e-12 | Sqle,Hmgcr,Cyp51,Fdft1,Fdps,Msmo1,Hmgcs1,Nsdhl,Dhcr7,Mvd,Pmvk,Sc5d |
| DE_genes_Cholangiocytes_KO_vs_WT | Metabolism of steroids | REAC:R-MMU-8957322 | 20 | 122 | 0.164 | 2.15e-10 | Gc,Sqle,Hmgcr,Cyp51,Fdft1,Fdps,Msmo1,Hmgcs1,Nsdhl,Dhcr7,Srebf2,Mvd,Pmvk,Sc5d,Alb,Serpina6,Akr1c6,Ran,Tspo,Hsd17b2 |
| DE_genes_Cholangiocytes_KO_vs_WT | Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | REAC:R-MMU-381426 | 19 | 111 | 0.171 | 3.75e-10 | Trf,C3,Igfbp4,Serpina10,Igfbp5,Gas6,Ahsg,Lgals1,Alb,Serpind1,Shisa5,Apob,Cdh2,Csf1,Kng2,Fgg,Fn1,Fga,Igf1 |
| DE_genes_Cholangiocytes_KO_vs_WT | Post-translational protein phosphorylation | REAC:R-MMU-8957275 | 18 | 105 | 0.171 | 1.48e-09 | Trf,C3,Igfbp4,Serpina10,Igfbp5,Gas6,Ahsg,Lgals1,Alb,Serpind1,Shisa5,Apob,Cdh2,Csf1,Kng2,Fgg,Fn1,Fga |
| DE_genes_Cholangiocytes_KO_vs_WT | Platelet degranulation | REAC:R-MMU-114608 | 16 | 110 | 0.145 | 3.04e-07 | Trf,Rab27b,Gas6,Ahsg,Vegfa,Alb,Sparc,Kng2,Apoh,Rarres2,Tgfb2,Tagln2,Fgg,Fn1,Fga,Igf1 |
| DE_genes_Cholangiocytes_KO_vs_WT | Response to elevated platelet cytosolic Ca2+ | REAC:R-MMU-76005 | 16 | 115 | 0.139 | 5.95e-07 | Trf,Rab27b,Gas6,Ahsg,Vegfa,Alb,Sparc,Kng2,Apoh,Rarres2,Tgfb2,Tagln2,Fgg,Fn1,Fga,Igf1 |
| DE_genes_Cholangiocytes_KO_vs_WT | Metabolism of lipids | REAC:R-MMU-556833 | 34 | 583 | 0.0583 | 1.3e-05 | Gc,Tbxas1,Fads1,Sqle,Hmgcr,Cyp51,Fdft1,Fdps,Msmo1,Hmgcs1,Scd2,Nsdhl,Elovl6,Dhcr7,Srebf2,Dbi,Degs2,Mvd,Mid1ip1,Pmvk,Sc5d,Gpx4,Cyp2d22,Alb,Serpina6,Gpx1,Hsd17b13,Akr1c6,Ran,Tspo,Plpp3,Fabp5,Hsd17b2,Ephx2 |
| DE_genes_Cholangiocytes_KO_vs_WT | Innate Immune System | REAC:R-MMU-168249 | 45 | 976 | 0.0461 | 7.06e-05 | Txnip,Pigr,C3,Anpep,H2-T23,Ahsg,Hp,H2-Q6,Crp,Cystm1,Ubc,Mme,Psmd8,Hspa8,H2-Q7,Cstb,Ctsh,H2-K1,Cfb,Nme2,Apob,Cpb2,Dynll1,F2,Atox1,Vtn,Psmb3,Psmb2,Psmb1,Psmb5,Bst2,Psma3,Mif,C4bp,Fgg,Tubb5,Fabp5,Cfi,Birc2,Fga,Lcn2,Itgav,Cpn1,Nfkbia,Stbd1 |
| DE_genes_Cholangiocytes_KO_vs_WT | Metabolism | REAC:R-MMU-1430728 | 63 | 1678 | 0.0375 | 0.00026 | Gc,Tbxas1,Fads1,Sqle,Hmgcr,Cyp51,Fdft1,Fdps,Msmo1,Hmgcs1,Scd2,Nsdhl,Elovl6,Dhcr7,Srebf2,Bgn,Dbi,Degs2,Mvd,Ces1d,Aldh1l1,Mid1ip1,Rbp1,Pmvk,Sc5d,Psmd8,Gpx4,Cyp2d22,Aldh1a1,Ndufa6,Slc2a2,Aldob,Alb,Cbs,Adk,St3gal4,Nme2,Serpina6,Gpx1,Apob,Qprt,Glo1,Psmb3,Fbp1,Nme1,Ces3a,Hsd17b13,Psmb2,Akr1c6,Psmb1,Psmb5,Nostrin,Ran,Psma3,Ext1,Tspo,Plpp3,Fabp5,Ddah1,Tst,Hsd17b2,Ephx2,Gamt |
| DE_genes_Cholangiocytes_KO_vs_WT | Platelet activation, signaling and aggregation | REAC:R-MMU-76002 | 18 | 239 | 0.0753 | 0.000827 | Trf,Rab27b,Gas6,Ahsg,Vegfa,Alb,Sparc,Rhob,F2,Kng2,Apoh,Rarres2,Tgfb2,Tagln2,Fgg,Fn1,Fga,Igf1 |
| DE_genes_Cholangiocytes_KO_vs_WT | AUF1 (hnRNP D0) binds and destabilizes mRNA | REAC:R-MMU-450408 | 9 | 58 | 0.155 | 0.00092 | Ubc,Psmd8,Hspa8,Hspb1,Psmb3,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Cholangiocytes_KO_vs_WT | Antigen processing-Cross presentation | REAC:R-MMU-1236975 | 11 | 95 | 0.116 | 0.00141 | H2-T23,H2-Q6,Psmd8,H2-Q7,H2-K1,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Itgav |
| DE_genes_Cholangiocytes_KO_vs_WT | Integrin cell surface interactions | REAC:R-MMU-216083 | 9 | 67 | 0.134 | 0.00314 | Vtn,Vcam1,Fgg,Col18a1,Fn1,Fga,Itgav,Icam1,Col4a1 |
| DE_genes_Cholangiocytes_KO_vs_WT | Regulation of mRNA stability by proteins that bind AU-rich elements | REAC:R-MMU-450531 | 10 | 85 | 0.118 | 0.00336 | Ubc,Psmd8,Hspa8,Hspb1,Psmb3,Zfp36,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Cholangiocytes_KO_vs_WT | Autodegradation of the E3 ubiquitin ligase COP1 | REAC:R-MMU-349425 | 8 | 54 | 0.148 | 0.00474 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Trp53 |
| DE_genes_Cholangiocytes_KO_vs_WT | Stabilization of p53 | REAC:R-MMU-69541 | 8 | 58 | 0.138 | 0.00812 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Trp53 |
| DE_genes_Cholangiocytes_KO_vs_WT | Activation of NF-kappaB in B cells | REAC:R-MMU-1169091 | 8 | 64 | 0.125 | 0.0168 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Nfkbia |
| DE_genes_Cholangiocytes_KO_vs_WT | p53-Dependent G1 DNA Damage Response | REAC:R-MMU-69563 | 8 | 67 | 0.119 | 0.0235 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Trp53 |
| DE_genes_Cholangiocytes_KO_vs_WT | p53-Dependent G1/S DNA damage checkpoint | REAC:R-MMU-69580 | 8 | 67 | 0.119 | 0.0235 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Trp53 |
| DE_genes_Cholangiocytes_KO_vs_WT | G1/S DNA Damage Checkpoints | REAC:R-MMU-69615 | 8 | 69 | 0.116 | 0.0291 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3,Trp53 |
| DE_genes_Cholangiocytes_KO_vs_WT | Regulation of RUNX2 expression and activity | REAC:R-MMU-8939902 | 7 | 53 | 0.132 | 0.0349 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Cholangiocytes_KO_vs_WT | Ubiquitin-dependent degradation of Cyclin D | REAC:R-MMU-75815 | 7 | 53 | 0.132 | 0.0349 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Cholangiocytes_KO_vs_WT | Hemostasis | REAC:R-MMU-109582 | 26 | 561 | 0.0463 | 0.0353 | Trf,Atp1b1,Kif12,Rab27b,Gas6,Ahsg,Cd74,Vegfa,Alb,Serpind1,Apob,Sparc,Rad51b,Rhob,F2,Kng2,Apoh,Rarres2,Tgfb2,Tagln2,Mif,Fgg,Fn1,Fga,Igf1,Itgav |
| DE_genes_Cholangiocytes_KO_vs_WT | p53-Independent DNA Damage Response | REAC:R-MMU-69610 | 7 | 54 | 0.13 | 0.0394 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Cholangiocytes_KO_vs_WT | p53-Independent G1/S DNA damage checkpoint | REAC:R-MMU-69613 | 7 | 54 | 0.13 | 0.0394 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Cholangiocytes_KO_vs_WT | Ubiquitin Mediated Degradation of Phosphorylated Cdc25A | REAC:R-MMU-69601 | 7 | 54 | 0.13 | 0.0394 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Cholangiocytes_KO_vs_WT | MAPK6/MAPK4 signaling | REAC:R-MMU-5687128 | 8 | 74 | 0.108 | 0.0479 | Ubc,Psmd8,Hspb1,Psmb3,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Cholangiocytes_KO_vs_WT | Regulation of RUNX3 expression and activity | REAC:R-MMU-8941858 | 7 | 56 | 0.125 | 0.0499 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Cholangiocytes_KO_vs_WT | Degradation of AXIN | REAC:R-MMU-4641257 | 7 | 56 | 0.125 | 0.0499 | Ubc,Psmd8,Psmb3,Psmb2,Psmb1,Psmb5,Psma3 |
| DE_genes_Endothelial_KO_vs_WT | PPAR signaling pathway | KEGG:03320 | 8 | 89 | 0.0899 | 8.07e-05 | Fabp1,Apoa2,Cd36,Apoc3,Apoa1,Scp2,Acaa1b,Dbi |
| DE_genes_Endothelial_KO_vs_WT | Metabolic pathways | KEGG:01100 | 31 | 1531 | 0.0202 | 0.000161 | Ass1,Gnmt,Gsta3,Hpd,Aldob,Alad,Car3,Gpx1,Rgn,Mat1a,Fbp1,Cth,Scp2,Uox,Arg1,Asl,Acaa1b,Urah,Atp5e,Otc,Cdo1,Pcbd1,mt-Nd4l,Gstm1,Cyp26b1,Tst,Adk,Prdx6,Sephs2,Mgst1,Oat |
| DE_genes_Endothelial_KO_vs_WT | Fluid shear stress and atherosclerosis | KEGG:05418 | 9 | 141 | 0.0638 | 0.000295 | Actg1,Ass1,Gsta3,Ctsl,Cyba,Il1a,Klf2,Gstm1,Mgst1 |
| DE_genes_Endothelial_KO_vs_WT | Biosynthesis of amino acids | KEGG:01230 | 7 | 77 | 0.0909 | 0.00037 | Ass1,Aldob,Mat1a,Cth,Arg1,Asl,Otc |
| DE_genes_Endothelial_KO_vs_WT | Arginine biosynthesis | KEGG:00220 | 4 | 20 | 0.2 | 0.00195 | Ass1,Arg1,Asl,Otc |
| DE_genes_Endothelial_KO_vs_WT | Cholesterol metabolism | KEGG:04979 | 5 | 49 | 0.102 | 0.00528 | Apoa2,Cd36,Apoc3,Apoc1,Apoa1 |
| DE_genes_Endothelial_KO_vs_WT | Glutathione metabolism | KEGG:00480 | 5 | 68 | 0.0735 | 0.0253 | Gsta3,Gpx1,Gstm1,Prdx6,Mgst1 |
| DE_genes_Endothelial_KO_vs_WT | Metabolism | REAC:R-MMU-1430728 | 40 | 1678 | 0.0238 | 2.1e-09 | Fabp1,Alb,Apoa2,Cd36,Ass1,Gnmt,Gsta3,Hpd,Gpihbp1,Ttr,Aldob,Rida,Alad,Rbp4,Car3,Gpx1,Mat1a,Apoa1,Thrsp,Stard10,Fbp1,Cth,Gc,Scp2,Arg1,Asl,Akr1c6,Lyve1,Atp5e,Otc,Cdo1,Pcbd1,Phyh,Cyp26b1,Tst,Adk,Sephs2,Dbi,Mgst1,Oat |
| DE_genes_Endothelial_KO_vs_WT | Platelet degranulation | REAC:R-MMU-114608 | 11 | 110 | 0.1 | 3.44e-07 | Alb,Sparc,Selenop,Actg1,Cd36,Cd9,Trf,Cd63,Apoa1,Ahsg,Lgals3bp |
| DE_genes_Endothelial_KO_vs_WT | Response to elevated platelet cytosolic Ca2+ | REAC:R-MMU-76005 | 11 | 115 | 0.0957 | 5.55e-07 | Alb,Sparc,Selenop,Actg1,Cd36,Cd9,Trf,Cd63,Apoa1,Ahsg,Lgals3bp |
| DE_genes_Endothelial_KO_vs_WT | Metabolism of amino acids and derivatives | REAC:R-MMU-71291 | 14 | 240 | 0.0583 | 1.99e-06 | Ass1,Gnmt,Hpd,Rida,Mat1a,Cth,Arg1,Asl,Otc,Cdo1,Pcbd1,Tst,Sephs2,Oat |
| DE_genes_Endothelial_KO_vs_WT | Platelet activation, signaling and aggregation | REAC:R-MMU-76002 | 12 | 239 | 0.0502 | 0.000136 | Alb,Sparc,Selenop,Actg1,Cd36,Cd9,Trf,Cd63,F2r,Apoa1,Ahsg,Lgals3bp |
| DE_genes_Endothelial_KO_vs_WT | Urea cycle | REAC:R-MMU-70635 | 4 | 10 | 0.4 | 0.000235 | Ass1,Arg1,Asl,Otc |
| DE_genes_Endothelial_KO_vs_WT | Retinoid metabolism and transport | REAC:R-MMU-975634 | 6 | 44 | 0.136 | 0.000387 | Apoa2,Gpihbp1,Ttr,Rbp4,Apoa1,Akr1c6 |
| DE_genes_Endothelial_KO_vs_WT | Metabolism of fat-soluble vitamins | REAC:R-MMU-6806667 | 6 | 49 | 0.122 | 0.000742 | Apoa2,Gpihbp1,Ttr,Rbp4,Apoa1,Akr1c6 |
| DE_genes_Endothelial_KO_vs_WT | Collagen degradation | REAC:R-MMU-1442490 | 6 | 53 | 0.113 | 0.00119 | Ctsl,Ctsb,Col4a2,Col4a1,Mmp14,Col5a2 |
| DE_genes_Endothelial_KO_vs_WT | Plasma lipoprotein assembly, remodeling, and clearance | REAC:R-MMU-174824 | 6 | 58 | 0.103 | 0.00202 | Alb,Apoa2,Gpihbp1,Apoc1,Apoa1,Apoc4 |
| DE_genes_Endothelial_KO_vs_WT | Plasma lipoprotein assembly | REAC:R-MMU-8963898 | 4 | 18 | 0.222 | 0.00326 | Apoa2,Apoc1,Apoa1,Apoc4 |
| DE_genes_Endothelial_KO_vs_WT | Metabolism of porphyrins | REAC:R-MMU-189445 | 4 | 23 | 0.174 | 0.00913 | Fabp1,Alb,Gsta3,Alad |
| DE_genes_Endothelial_KO_vs_WT | Extracellular matrix organization | REAC:R-MMU-1474244 | 10 | 253 | 0.0395 | 0.0108 | Sparc,Ttr,Ctsl,Ctsb,Emilin1,Col4a2,Col4a1,Icam2,Mmp14,Col5a2 |
| DE_genes_Endothelial_KO_vs_WT | Sulfur amino acid metabolism | REAC:R-MMU-1614635 | 4 | 24 | 0.167 | 0.0109 | Mat1a,Cth,Cdo1,Tst |
| DE_genes_Endothelial_KO_vs_WT | Plasma lipoprotein remodeling | REAC:R-MMU-8963899 | 4 | 25 | 0.16 | 0.0129 | Alb,Apoa2,Gpihbp1,Apoa1 |
| DE_genes_Endothelial_KO_vs_WT | Chylomicron remodeling | REAC:R-MMU-8963901 | 3 | 10 | 0.3 | 0.0168 | Apoa2,Gpihbp1,Apoa1 |
| DE_genes_Endothelial_KO_vs_WT | Assembly of collagen fibrils and other multimeric structures | REAC:R-MMU-2022090 | 5 | 54 | 0.0926 | 0.021 | Ctsl,Ctsb,Col4a2,Col4a1,Col5a2 |
| DE_genes_Endothelial_KO_vs_WT | Trafficking and processing of endosomal TLR | REAC:R-MMU-1679131 | 3 | 11 | 0.273 | 0.023 | Ctsl,Lgmn,Ctsb |
| DE_genes_Endothelial_KO_vs_WT | Visual phototransduction | REAC:R-MMU-2187338 | 6 | 91 | 0.0659 | 0.0269 | Apoa2,Gpihbp1,Ttr,Rbp4,Apoa1,Akr1c6 |
| DE_genes_Endothelial_KO_vs_WT | Heme degradation | REAC:R-MMU-189483 | 3 | 12 | 0.25 | 0.0305 | Fabp1,Alb,Gsta3 |
| DE_genes_Endothelial_KO_vs_WT | Degradation of cysteine and homocysteine | REAC:R-MMU-1614558 | 3 | 12 | 0.25 | 0.0305 | Cth,Cdo1,Tst |
| DE_genes_Endothelial_KO_vs_WT | Non-integrin membrane-ECM interactions | REAC:R-MMU-3000171 | 4 | 34 | 0.118 | 0.0446 | Ttr,Col4a2,Col4a1,Col5a2 |
| DE_genes_Hepatocytes_KO_vs_WT | Metabolic pathways | KEGG:01100 | 77 | 1531 | 0.0503 | 9.87e-17 | Selenbp2,Aox3,Car3,Hpd,Asl,Mat1a,Gstt3,Pck1,Cyp2e1,Gnmt,Elovl3,Got1,Alas2,Nnmt,Ass1,Aldob,Cth,Gsta2,Gstm3,Gstm1,Hsd3b5,Cbr1,Aldh2,Nme2,Hao2,Gm3776,Keg1,Rdh16f2,Acnat2,Pank1,Acot3,Gstk1,Gls2,Acot1,Cyp3a11,Alas1,Papss2,Tat,Acaa1b,Gstt1,Cyp4a12a,Cyp2c40,Fbp1,Kyat3,Alad,Acadl,Cyp3a44,Oat,Cyp2a4,Mgst1,Gsta1,Sds,Upp2,Ugp2,Acot4,Grhpr,Car5a,Hadh,Cyp2c50,Mocs2,Aass,Nadk,Selenbp1,Me1,Paics,Acmsd,Nat8f2,Cyp2a5,Sord,Agmat,Aldh8a1,Aldh3a2,Akr1d1,Etnppl,Coq7,Hao1,Gclc |
| DE_genes_Hepatocytes_KO_vs_WT | Chemical carcinogenesis | KEGG:05204 | 20 | 96 | 0.208 | 5.36e-14 | Gstt3,Sult2a5,Sult2a1,Cyp2e1,Sult1a1,Gsta2,Gstm3,Gstm1,Cbr1,Gm3776,Gstk1,Cyp3a11,Gstt1,Cyp2c40,Kyat3,Cyp3a44,Mgst1,Gsta1,Cyp2c50,Sult2a8 |
| DE_genes_Hepatocytes_KO_vs_WT | Drug metabolism - cytochrome P450 | KEGG:00982 | 14 | 67 | 0.209 | 1.51e-09 | Aox3,Gstt3,Cyp2e1,Fmo3,Gsta2,Gstm3,Gstm1,Gm3776,Gstk1,Gstt1,Mgst1,Gsta1,Fmo1,Fmo2 |
| DE_genes_Hepatocytes_KO_vs_WT | Metabolism of xenobiotics by cytochrome P450 | KEGG:00980 | 14 | 69 | 0.203 | 2.3e-09 | Gstt3,Sult2a5,Sult2a1,Cyp2e1,Gsta2,Gstm3,Gstm1,Cbr1,Gm3776,Gstk1,Gstt1,Mgst1,Gsta1,Sult2a8 |
| DE_genes_Hepatocytes_KO_vs_WT | Glutathione metabolism | KEGG:00480 | 11 | 68 | 0.162 | 4.22e-06 | Gstt3,Gsta2,Gstm3,Gstm1,Gm3776,Gstk1,Gstt1,Mgst1,Gsta1,Nat8f2,Gclc |
| DE_genes_Hepatocytes_KO_vs_WT | Drug metabolism - other enzymes | KEGG:00983 | 12 | 88 | 0.136 | 7.26e-06 | Gstt3,Cyp2e1,Gsta2,Gstm3,Gstm1,Nme2,Gm3776,Gstt1,Mgst1,Gsta1,Upp2,Tpmt |
| DE_genes_Hepatocytes_KO_vs_WT | Biosynthesis of cofactors | KEGG:01240 | 15 | 150 | 0.1 | 1.14e-05 | Hpd,Mat1a,Alas2,Aldh2,Nme2,Pank1,Alas1,Alad,Ugp2,Mocs2,Nadk,Ak3,Aldh3a2,Coq7,Gclc |
| DE_genes_Hepatocytes_KO_vs_WT | Fluid shear stress and atherosclerosis | KEGG:05418 | 13 | 141 | 0.0922 | 0.000209 | Gstt3,Ass1,Hsp90ab1,Gsta2,Gstm3,Gstm1,Jun,Gm3776,Actb,Gstt1,Mgst1,Gsta1,Actg1 |
| DE_genes_Hepatocytes_KO_vs_WT | Platinum drug resistance | KEGG:01524 | 9 | 76 | 0.118 | 0.00108 | Gstt3,Gsta2,Gstm3,Gstm1,Gm3776,Cdkn1a,Gstt1,Mgst1,Gsta1 |
| DE_genes_Hepatocytes_KO_vs_WT | Peroxisome | KEGG:04146 | 9 | 84 | 0.107 | 0.00245 | Nudt7,Hacl1,Ech1,Hao2,Acnat2,Gstk1,Acaa1b,Prdx5,Hao1 |
| DE_genes_Hepatocytes_KO_vs_WT | Biosynthesis of unsaturated fatty acids | KEGG:01040 | 6 | 34 | 0.176 | 0.00334 | Elovl3,Acnat2,Acot3,Acot1,Acaa1b,Acot4 |
| DE_genes_Hepatocytes_KO_vs_WT | Steroid hormone biosynthesis | KEGG:00140 | 9 | 88 | 0.102 | 0.00357 | Cyp2e1,Hsd3b5,Cyp2d9,Cyp3a11,Cyp2c40,Cyp3a44,Cyp2d40,Cyp2c50,Akr1d1 |
| DE_genes_Hepatocytes_KO_vs_WT | Tryptophan metabolism | KEGG:00380 | 7 | 51 | 0.137 | 0.00401 | Aox3,Aldh2,Kyat3,Hadh,Acmsd,Aldh8a1,Aldh3a2 |
| DE_genes_Hepatocytes_KO_vs_WT | Cysteine and methionine metabolism | KEGG:00270 | 7 | 51 | 0.137 | 0.00401 | Mat1a,Got1,Cth,Tat,Kyat3,Sds,Gclc |
| DE_genes_Hepatocytes_KO_vs_WT | Retinol metabolism | KEGG:00830 | 9 | 94 | 0.0957 | 0.00604 | Aox3,Rdh16f2,Cyp3a11,Cyp4a12a,Cyp2c40,Cyp3a44,Cyp2a4,Cyp2c50,Cyp2a5 |
| DE_genes_Hepatocytes_KO_vs_WT | Glycine, serine and threonine metabolism | KEGG:00260 | 6 | 38 | 0.158 | 0.00644 | Gnmt,Alas2,Cth,Alas1,Sds,Grhpr |
| DE_genes_Hepatocytes_KO_vs_WT | Fatty acid elongation | KEGG:00062 | 5 | 29 | 0.172 | 0.0174 | Elovl3,Acot3,Acot1,Acot4,Hadh |
| DE_genes_Hepatocytes_KO_vs_WT | Hepatocellular carcinoma | KEGG:05225 | 11 | 165 | 0.0667 | 0.0253 | Gstt3,Gsta2,Gstm3,Gstm1,Gm3776,Cdkn1a,Actb,Gstt1,Mgst1,Gsta1,Actg1 |
| DE_genes_Hepatocytes_KO_vs_WT | Complement and coagulation cascades | KEGG:04610 | 8 | 91 | 0.0879 | 0.0282 | Serpina1d,Serpina1c,Serpina1a,Serpina1b,Clu,C4bp,Vtn,Fgb |
| DE_genes_Hepatocytes_KO_vs_WT | Fatty acid degradation | KEGG:00071 | 6 | 51 | 0.118 | 0.0344 | Aldh2,Acaa1b,Cyp4a12a,Acadl,Hadh,Aldh3a2 |
| DE_genes_Hepatocytes_KO_vs_WT | Arginine biosynthesis | KEGG:00220 | 4 | 20 | 0.2 | 0.0442 | Asl,Got1,Ass1,Gls2 |
| DE_genes_Hepatocytes_KO_vs_WT | Metabolism | REAC:R-MMU-1430728 | 77 | 1678 | 0.0459 | 5.52e-19 | Nudt7,Car3,Hpd,Asl,Mat1a,Thrsp,Pck1,Cyp2e1,Gnmt,Elovl3,Got1,Alas2,Nnmt,Ass1,Aldob,Alb,Fmo3,Hsp90ab1,Cth,Hsd3b5,Fabp5,Rida,Cbr1,Aldh2,Hacl1,Nme2,Hao2,Hpgd,Rbp1,Pank1,Acot3,Gstk1,Gls2,Acot1,Cyp3a11,Alas1,Papss2,Tat,Gstt1,Cyp4a12a,Fbp1,Akr1c6,Alad,Cyp3a44,Oat,Fitm1,Cyp2a4,Mgst1,Apoa1,Gsta1,Sds,Upp2,Ugp2,Acot4,Grhpr,Car5a,Hadh,Slc25a15,Aass,Nadk,Me1,Paics,Fmo1,Gchfr,Fmo2,Sord,Agmat,Pon1,Aldh3a2,Akr1d1,As3mt,Tstd1,Etnppl,Hao1,Gclc,Psmb8,Apoe |
| DE_genes_Hepatocytes_KO_vs_WT | Biological oxidations | REAC:R-MMU-211859 | 20 | 204 | 0.098 | 1.95e-08 | Mat1a,Cyp2e1,Nnmt,Fmo3,Hsp90ab1,Aldh2,Gstk1,Cyp3a11,Papss2,Gstt1,Cyp4a12a,Cyp3a44,Cyp2a4,Mgst1,Gsta1,Ugp2,Fmo1,Fmo2,As3mt,Gclc |
| DE_genes_Hepatocytes_KO_vs_WT | Protein localization | REAC:R-MMU-9609507 | 14 | 100 | 0.14 | 1.58e-07 | Nudt7,Hacl1,Ech1,Hao2,Hspd1,Ubb,Acot3,Gstk1,Acot1,Sec61g,Acot4,Sec61b,Aldh3a2,Hao1 |
| DE_genes_Hepatocytes_KO_vs_WT | Metabolism of amino acids and derivatives | REAC:R-MMU-71291 | 19 | 240 | 0.0792 | 2.29e-06 | Hpd,Asl,Mat1a,Gnmt,Got1,Ass1,Cth,Rida,Gls2,Tat,Oat,Sds,Grhpr,Slc25a15,Aass,Agmat,Tstd1,Hao1,Psmb8 |
| DE_genes_Hepatocytes_KO_vs_WT | Peroxisomal protein import | REAC:R-MMU-9033241 | 10 | 63 | 0.159 | 1.53e-05 | Nudt7,Hacl1,Ech1,Hao2,Ubb,Acot3,Gstk1,Acot1,Acot4,Hao1 |
| DE_genes_Hepatocytes_KO_vs_WT | Fatty acid metabolism | REAC:R-MMU-8978868 | 14 | 168 | 0.0833 | 0.000133 | Nudt7,Thrsp,Elovl3,Cbr1,Hacl1,Hao2,Acot3,Acot1,Cyp4a12a,Akr1c6,Acot4,Hadh,Pon1,Aldh3a2 |
| DE_genes_Hepatocytes_KO_vs_WT | Phase II - Conjugation of compounds | REAC:R-MMU-156580 | 10 | 92 | 0.109 | 0.000581 | Mat1a,Nnmt,Gstk1,Papss2,Gstt1,Mgst1,Gsta1,Ugp2,As3mt,Gclc |
| DE_genes_Hepatocytes_KO_vs_WT | FMO oxidises nucleophiles | REAC:R-MMU-217271 | 3 | 3 | 1 | 0.00124 | Fmo3,Fmo1,Fmo2 |
| DE_genes_Hepatocytes_KO_vs_WT | Phase I - Functionalization of compounds | REAC:R-MMU-211945 | 10 | 106 | 0.0943 | 0.00212 | Cyp2e1,Fmo3,Hsp90ab1,Aldh2,Cyp3a11,Cyp4a12a,Cyp3a44,Cyp2a4,Fmo1,Fmo2 |
| DE_genes_Hepatocytes_KO_vs_WT | Heme biosynthesis | REAC:R-MMU-189451 | 4 | 12 | 0.333 | 0.00869 | Alas2,Alb,Alas1,Alad |
| DE_genes_Hepatocytes_KO_vs_WT | Platelet degranulation | REAC:R-MMU-114608 | 9 | 110 | 0.0818 | 0.0194 | Alb,Anxa5,Apoa1,Tagln2,Clu,Tmsb4x,Rarres2,Actg1,Fgb |
| DE_genes_Hepatocytes_KO_vs_WT | Peroxisomal lipid metabolism | REAC:R-MMU-390918 | 5 | 29 | 0.172 | 0.0263 | Nudt7,Hacl1,Hao2,Acot4,Aldh3a2 |
| DE_genes_Hepatocytes_KO_vs_WT | Response to elevated platelet cytosolic Ca2+ | REAC:R-MMU-76005 | 9 | 115 | 0.0783 | 0.0275 | Alb,Anxa5,Apoa1,Tagln2,Clu,Tmsb4x,Rarres2,Actg1,Fgb |
| DE_genes_Hepatocytes_KO_vs_WT | Metabolism of lipids | REAC:R-MMU-556833 | 22 | 583 | 0.0377 | 0.041 | Nudt7,Thrsp,Cyp2e1,Elovl3,Alb,Hsd3b5,Fabp5,Cbr1,Hacl1,Hao2,Hpgd,Acot3,Acot1,Cyp4a12a,Akr1c6,Fitm1,Acot4,Hadh,Pon1,Aldh3a2,Akr1d1,Etnppl |
| DE_genes_Hepatocytes_KO_vs_WT | Glutathione conjugation | REAC:R-MMU-156590 | 5 | 32 | 0.156 | 0.0429 | Gstk1,Gstt1,Mgst1,Gsta1,Gclc |
| DE_genes_HSC & PF_KO_vs_WT | Focal adhesion | KEGG:04510 | 19 | 196 | 0.0969 | 1.07e-05 | Itga8,Actg1,Pdgfrb,Mylk,Col4a2,Actb,Col6a1,Col6a3,Col6a2,Col1a1,Igf1,Vasp,Vegfc,Col4a1,Actn1,Fn1,Ccnd2,Col6a5,Kdr |
| DE_genes_HSC & PF_KO_vs_WT | Fluid shear stress and atherosclerosis | KEGG:05418 | 15 | 141 | 0.106 | 7.51e-05 | Actg1,Gsta3,Actb,Ass1,Il1r1,Mmp2,Tnfrsf1a,Vcam1,Sdc2,Hmox1,Fos,Sdc4,Dusp1,Kdr,Klf2 |
| DE_genes_HSC & PF_KO_vs_WT | ECM-receptor interaction | KEGG:04512 | 10 | 87 | 0.115 | 0.00277 | Itga8,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Col4a1,Sdc4,Fn1,Col6a5 |
| DE_genes_HSC & PF_KO_vs_WT | PPAR signaling pathway | KEGG:03320 | 10 | 89 | 0.112 | 0.00339 | Lpl,Fabp1,Apoa2,Hmgcs2,Acaa1b,Apoc3,Scp2,Apoa1,Dbi,Fabp4 |
| DE_genes_HSC & PF_KO_vs_WT | Complement and coagulation cascades | KEGG:04610 | 10 | 91 | 0.11 | 0.00411 | Serpina1c,C4b,Serpina1a,Masp1,Pros1,C6,C3,Cfb,Cd59a,Serpina1b |
| DE_genes_HSC & PF_KO_vs_WT | Cholesterol metabolism | KEGG:04979 | 7 | 49 | 0.143 | 0.0112 | Lpl,Apoe,Apoa2,Vdac2,Apoc3,Apoc1,Apoa1 |
| DE_genes_HSC & PF_KO_vs_WT | AGE-RAGE signaling pathway in diabetic complications | KEGG:04933 | 9 | 99 | 0.0909 | 0.0424 | Col3a1,Col4a2,Col1a1,Mmp2,Vcam1,Vegfc,Col4a1,Egr1,Fn1 |
| DE_genes_HSC & PF_KO_vs_WT | Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | REAC:R-MMU-381426 | 25 | 111 | 0.225 | 2.68e-16 | C4b,Apoe,Sparcl1,Cst3,Scg2,Scg3,Chgb,Apoa2,Gas6,Cp,Igf1,Igfbp4,Fstl1,Mxra8,Alb,Sdc2,Igfbp6,Timp1,Ltbp1,C3,Apoa1,Fn1,Igfbp5,Ahsg,Igfbp3 |
| DE_genes_HSC & PF_KO_vs_WT | Post-translational protein phosphorylation | REAC:R-MMU-8957275 | 23 | 105 | 0.219 | 1.41e-14 | C4b,Apoe,Sparcl1,Cst3,Scg2,Scg3,Chgb,Apoa2,Gas6,Cp,Igfbp4,Fstl1,Mxra8,Alb,Sdc2,Timp1,Ltbp1,C3,Apoa1,Fn1,Igfbp5,Ahsg,Igfbp3 |
| DE_genes_HSC & PF_KO_vs_WT | Platelet degranulation | REAC:R-MMU-114608 | 21 | 110 | 0.191 | 6.74e-12 | Islr,Actg1,Scg3,Lamp2,Gas6,Igf1,Cd9,Sparc,Tagln2,Cd63,Alb,Vegfc,Selenop,Pros1,Pf4,Actn1,Timp1,Apoa1,Fn1,Ahsg,Ecm1 |
| DE_genes_HSC & PF_KO_vs_WT | Extracellular matrix organization | REAC:R-MMU-1474244 | 30 | 253 | 0.119 | 9.16e-12 | Lum,Itga8,Col3a1,Serpinh1,Emilin1,Fbln5,Ttr,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Mmp2,Ppib,Adamts5,Sparc,Efemp2,Adamts2,Htra1,Jam2,Vcam1,Mmp14,Sdc2,Col4a1,Col5a2,Ctsk,Timp1,Ltbp1,Sdc4,Fn1 |
| DE_genes_HSC & PF_KO_vs_WT | Response to elevated platelet cytosolic Ca2+ | REAC:R-MMU-76005 | 21 | 115 | 0.183 | 1.71e-11 | Islr,Actg1,Scg3,Lamp2,Gas6,Igf1,Cd9,Sparc,Tagln2,Cd63,Alb,Vegfc,Selenop,Pros1,Pf4,Actn1,Timp1,Apoa1,Fn1,Ahsg,Ecm1 |
| DE_genes_HSC & PF_KO_vs_WT | Integrin cell surface interactions | REAC:R-MMU-216083 | 13 | 67 | 0.194 | 6.18e-07 | Lum,Itga8,Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Jam2,Vcam1,Col4a1,Col5a2,Fn1 |
| DE_genes_HSC & PF_KO_vs_WT | Platelet activation, signaling and aggregation | REAC:R-MMU-76002 | 23 | 239 | 0.0962 | 8.14e-07 | Islr,Actg1,Scg3,Lamp2,Col1a1,Gas6,Rhob,Igf1,Cd9,Sparc,Tagln2,Cd63,Alb,Vegfc,Selenop,Pros1,Pf4,Actn1,Timp1,Apoa1,Fn1,Ahsg,Ecm1 |
| DE_genes_HSC & PF_KO_vs_WT | Collagen degradation | REAC:R-MMU-1442490 | 11 | 53 | 0.208 | 5.42e-06 | Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Mmp2,Mmp14,Col4a1,Col5a2,Ctsk |
| DE_genes_HSC & PF_KO_vs_WT | Non-integrin membrane-ECM interactions | REAC:R-MMU-3000171 | 9 | 34 | 0.265 | 1.17e-05 | Col3a1,Ttr,Col4a2,Col1a1,Sdc2,Col4a1,Col5a2,Sdc4,Fn1 |
| DE_genes_HSC & PF_KO_vs_WT | Collagen biosynthesis and modifying enzymes | REAC:R-MMU-1650814 | 11 | 59 | 0.186 | 1.77e-05 | Col3a1,Serpinh1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Ppib,Adamts2,Col4a1,Col5a2 |
| DE_genes_HSC & PF_KO_vs_WT | Degradation of the extracellular matrix | REAC:R-MMU-1474228 | 15 | 121 | 0.124 | 2.04e-05 | Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Mmp2,Adamts5,Htra1,Mmp14,Col4a1,Col5a2,Ctsk,Timp1,Fn1 |
| DE_genes_HSC & PF_KO_vs_WT | NCAM1 interactions | REAC:R-MMU-419037 | 7 | 18 | 0.389 | 2.07e-05 | Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col4a1,Col5a2 |
| DE_genes_HSC & PF_KO_vs_WT | ECM proteoglycans | REAC:R-MMU-3000178 | 9 | 40 | 0.225 | 5.46e-05 | Itga8,Col3a1,Col6a1,Col6a3,Col6a2,Col1a1,Sparc,Col5a2,Fn1 |
| DE_genes_HSC & PF_KO_vs_WT | NCAM signaling for neurite out-growth | REAC:R-MMU-375165 | 8 | 34 | 0.235 | 0.000189 | Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col4a1,Col5a2,Sptbn1 |
| DE_genes_HSC & PF_KO_vs_WT | Collagen formation | REAC:R-MMU-1474290 | 11 | 79 | 0.139 | 0.000389 | Col3a1,Serpinh1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Ppib,Adamts2,Col4a1,Col5a2 |
| DE_genes_HSC & PF_KO_vs_WT | Collagen chain trimerization | REAC:R-MMU-8948216 | 8 | 38 | 0.211 | 0.000471 | Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Col4a1,Col5a2 |
| DE_genes_HSC & PF_KO_vs_WT | Retinoid metabolism and transport | REAC:R-MMU-975634 | 8 | 44 | 0.182 | 0.00152 | Lpl,Apoe,Ttr,Apoa2,Rbp4,Sdc2,Sdc4,Apoa1 |
| DE_genes_HSC & PF_KO_vs_WT | Hemostasis | REAC:R-MMU-109582 | 30 | 561 | 0.0535 | 0.00175 | H3f3b,Islr,Actg1,Scg3,Lamp2,Col1a1,Gas6,Rhob,Igf1,Cd9,Epcam,Sparc,Tagln2,Cd63,Alb,Jam2,Vegfc,Sdc2,Selenop,Pros1,Pf4,Actn1,Timp1,Sdc4,Apoa1,Fn1,Ahsg,Ehd3,Ecm1,Cd74 |
| DE_genes_HSC & PF_KO_vs_WT | Metabolism of fat-soluble vitamins | REAC:R-MMU-6806667 | 8 | 49 | 0.163 | 0.00353 | Lpl,Apoe,Ttr,Apoa2,Rbp4,Sdc2,Sdc4,Apoa1 |
| DE_genes_HSC & PF_KO_vs_WT | Cell-extracellular matrix interactions | REAC:R-MMU-446353 | 5 | 15 | 0.333 | 0.00434 | Actg1,Actb,Vasp,Actn1,Fblim1 |
| DE_genes_HSC & PF_KO_vs_WT | Nervous system development | REAC:R-MMU-9675108 | 18 | 256 | 0.0703 | 0.00469 | Col3a1,Actg1,Col4a2,Actb,Col6a1,Cxcl12,Col6a3,Col6a2,Gfra2,Rhob,Mmp2,Vasp,Sdc2,Col4a1,Col5a2,Plxna4,Sptbn1,Ezr |
| DE_genes_HSC & PF_KO_vs_WT | Axon guidance | REAC:R-MMU-422475 | 18 | 256 | 0.0703 | 0.00469 | Col3a1,Actg1,Col4a2,Actb,Col6a1,Cxcl12,Col6a3,Col6a2,Gfra2,Rhob,Mmp2,Vasp,Sdc2,Col4a1,Col5a2,Plxna4,Sptbn1,Ezr |
| DE_genes_HSC & PF_KO_vs_WT | Signaling by PDGF | REAC:R-MMU-186797 | 8 | 52 | 0.154 | 0.00557 | Col3a1,Pdgfrb,Col4a2,Col6a1,Col6a3,Col6a2,Col4a1,Col5a2 |
| DE_genes_HSC & PF_KO_vs_WT | Assembly of collagen fibrils and other multimeric structures | REAC:R-MMU-2022090 | 8 | 54 | 0.148 | 0.00741 | Col3a1,Col4a2,Col6a1,Col6a3,Col6a2,Col1a1,Col4a1,Col5a2 |
| DE_genes_HSC & PF_KO_vs_WT | Plasma lipoprotein assembly | REAC:R-MMU-8963898 | 5 | 18 | 0.278 | 0.0117 | Apoe,Apoa2,Apoc4,Apoc1,Apoa1 |
| DE_genes_HSC & PF_KO_vs_WT | Chylomicron remodeling | REAC:R-MMU-8963901 | 4 | 10 | 0.4 | 0.0151 | Lpl,Apoe,Apoa2,Apoa1 |
| DE_genes_HSC & PF_KO_vs_WT | Molecules associated with elastic fibres | REAC:R-MMU-2129379 | 6 | 31 | 0.194 | 0.0173 | Itga8,Emilin1,Fbln5,Efemp2,Ltbp1,Fn1 |
| DE_genes_HSC & PF_KO_vs_WT | Heme degradation | REAC:R-MMU-189483 | 4 | 12 | 0.333 | 0.0344 | Fabp1,Gsta3,Alb,Hmox1 |
| DE_genes_HSC & PF_KO_vs_WT | Metabolism of porphyrins | REAC:R-MMU-189445 | 5 | 23 | 0.217 | 0.0421 | Fabp1,Alad,Gsta3,Alb,Hmox1 |
| DE_genes_HSC & PF_KO_vs_WT | Elastic fibre formation | REAC:R-MMU-1566948 | 6 | 37 | 0.162 | 0.0489 | Itga8,Emilin1,Fbln5,Efemp2,Ltbp1,Fn1 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Complement and coagulation cascades | KEGG:04610 | 9 | 91 | 0.0989 | 4.27e-05 | C6,C4b,Cfh,C2,Serpina1c,Vsig4,Clu,Serpina1a,Serpina1b |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Staphylococcus aureus infection | KEGG:05150 | 9 | 116 | 0.0776 | 0.000333 | C4b,Fpr1,Cfh,C2,Itgal,Krt18,H2-Ab1,H2-Aa,H2-Eb1 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | PPAR signaling pathway | KEGG:03320 | 8 | 89 | 0.0899 | 0.000396 | Apoa2,Cd36,Rxra,Fabp5,Apoc3,Lpl,Fabp1,Apoa1 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Phagosome | KEGG:04145 | 10 | 173 | 0.0578 | 0.00132 | Cd209g,Cd209f,H2-D1,Cd36,Mrc1,Tubb5,Coro1a,H2-Ab1,H2-Aa,H2-Eb1 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Tuberculosis | KEGG:05152 | 10 | 179 | 0.0559 | 0.00177 | Cd209g,Cd209f,Mrc1,Ifngr1,Ctsd,Lsp1,Coro1a,H2-Ab1,H2-Aa,H2-Eb1 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Viral protein interaction with cytokine and cytokine receptor | KEGG:04061 | 7 | 92 | 0.0761 | 0.0048 | Ccl6,Cxcl13,Ccr3,Ccl24,Cx3cr1,Cxcl14,Ccr2 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Epstein-Barr virus infection | KEGG:05169 | 10 | 221 | 0.0452 | 0.0106 | B2m,H2-D1,Itgal,Hes1,Blnk,Vim,Gadd45b,H2-Ab1,H2-Aa,H2-Eb1 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Cholesterol metabolism | KEGG:04979 | 5 | 49 | 0.102 | 0.0148 | Apoa2,Cd36,Apoc3,Lpl,Apoa1 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Inflammatory bowel disease | KEGG:05321 | 5 | 61 | 0.082 | 0.0418 | Maf,Ifngr1,H2-Ab1,H2-Aa,H2-Eb1 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Neutrophil degranulation | REAC:R-MMU-6798695 | 22 | 517 | 0.0426 | 7.63e-07 | Cd63,B2m,Fcna,Ctsc,Cfp,Fpr1,Lilra5,Anxa2,Cd36,Fabp5,Pira2,Itgal,Nme2,Ctsd,Cstb,Hexb,Gsn,Fth1,Cd300c2,Tubb5,Vat1,Plac8 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Innate Immune System | REAC:R-MMU-168249 | 30 | 976 | 0.0307 | 1.15e-06 | Cd63,C6,B2m,Fcna,C4b,Ctsc,Cfp,Fpr1,Cfh,Lilra5,Txnip,Anxa2,Cd36,C2,Fabp5,Pira2,Itgal,Nme2,Ctsd,Cstb,Clu,Hexb,Gsn,Fth1,Cd300c2,Pld3,Tubb5,Ctnnb1,Vat1,Plac8 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Post-translational protein phosphorylation | REAC:R-MMU-8957275 | 10 | 105 | 0.0952 | 1.83e-05 | C4b,Lgals1,Trf,Alb,Apoa2,Spp1,Fam20c,Apoa1,Ccn1,Cp |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Platelet degranulation | REAC:R-MMU-114608 | 10 | 110 | 0.0909 | 2.86e-05 | Cd63,Cd9,Trf,Alb,Cd36,Tagln2,Clu,Apoa1,Anxa5,Sparc |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) | REAC:R-MMU-381426 | 10 | 111 | 0.0901 | 3.12e-05 | C4b,Lgals1,Trf,Alb,Apoa2,Spp1,Fam20c,Apoa1,Ccn1,Cp |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Response to elevated platelet cytosolic Ca2+ | REAC:R-MMU-76005 | 10 | 115 | 0.087 | 4.37e-05 | Cd63,Cd9,Trf,Alb,Cd36,Tagln2,Clu,Apoa1,Anxa5,Sparc |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Chylomicron remodeling | REAC:R-MMU-8963901 | 4 | 10 | 0.4 | 0.000493 | Apoa2,Lpl,Apoa1,Gpihbp1 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Plasma lipoprotein remodeling | REAC:R-MMU-8963899 | 5 | 25 | 0.2 | 0.00104 | Alb,Apoa2,Lpl,Apoa1,Gpihbp1 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Immune System | REAC:R-MMU-168256 | 35 | 1737 | 0.0201 | 0.00171 | Cd63,C6,B2m,Fcna,C4b,Ctsc,Cfp,Fpr1,Cfh,Lilra5,Txnip,Anxa2,Cd36,C2,Fabp5,Mrc1,Pira2,Itgal,Nme2,Ifngr1,Ctsd,Cstb,Clu,Hexb,Il1rn,Gsn,Fth1,Cd300c2,Pld3,Blnk,Tubb5,Ctnnb1,Vat1,Dusp1,Plac8 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Activation of C3 and C5 | REAC:R-MMU-174577 | 3 | 7 | 0.429 | 0.00885 | C4b,Cfp,C2 |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Complement cascade | REAC:R-MMU-166658 | 7 | 109 | 0.0642 | 0.0257 | C6,Fcna,C4b,Cfp,Cfh,C2,Clu |
| DE_genes_Macrophage_Kupffer_KO_vs_WT | Platelet activation, signaling and aggregation | REAC:R-MMU-76002 | 10 | 239 | 0.0418 | 0.0304 | Cd63,Cd9,Trf,Alb,Cd36,Tagln2,Clu,Apoa1,Anxa5,Sparc |
For pathway analysis, the R package gprofiler2 v0.2.0 was employed. Graphs were produced in RStudio with R version 4.0.3 (2020-10-10) mainly using the R package ggplot2 v3.3.2. Final reports were produced using the R package rmarkdown v2.6, with knitr v1.30.